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Searches - Help

Understanding How Quertle's BioAI™ Products Discover Documents
To give you the most relevant and focused results, BioAI™ uses artificial intelligence and natural language understanding to identify documents where the author(s) imply a meaningful connection among your search terms, not just documents that contain your query terms anywhere. For example, if your query is for "caffeine migraine", you will find documents in which the author has stated that there is a relationship between both terms, such as "caffeine treats migraines". This enables you to find the most relevant documents, and not get overwhelmed by the ones that happen to use both of the search terms, but not in a meaningful connection.

BioAI™ separately does a keyword search for documents that contain all of your search terms independent of whether there is a meaningful connection. This keyword search looks not only at the author's text, but also metadata, such as the MeSH Headings. These "Broader" results are presented on a separate tab on results page if you need them, but generally the "Focused" results are more valuable.

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Query Basics
Creating a query is simple. Just enter the term(s) of interest in the main search box and click Search or use your keyboard Enter key. BioAI™ uses an advanced ontology of biological, medical, and chemical terms, so it is just fine to use the form you are most comfortable with and BioAI™ will find all the synonyms automatically. The ontology also enables recognition of multiple word phrases (such as "cell cycle") that convey a single concept.

Generally, to find the best results, your query should focus on the core concept(s) of interest, leaving additional restricting terms for filtering on the results page.

Use the main search box (the top and largest entry area) for the terms that would likely be in the informative text of the documents. Leave additional components, such as Authors, Journals, or Affiliations for their specific entry areas. Similarly, leave qualifiers, such as Publication Type (e.g., "Review") or Publication Date for those specific filters on the Results page. Not all components are available to all subscription levels. For Qinsight subscribers, there are several patent-specific search fields that can be seen after clicking "Show Additional Patent Search Options +".

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Search just the one or two most important concepts at first, then use Author, Journal, Affiliation or the filters on the Results page to focus in further.

At this time, BioAI™ supports only queries in English. Both American and British forms of words, such as "hematoma" and "haematoma", are acceptable.

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Query Structure
The text part of your search query should be entered in the main search box - the largest search box (the one with the Search button). This part of your search query should focus on the core concept you are looking for. Save other components, such as "Review" or dates for later. It is generally more fruitful to save additional qualifying terms until after you have the first set of results. Then, the qualifying terms can be added using the Also Containing or Not Containing filters, or you may find the Key Concept filter and, for Qinsight only, the Visual Analytics to be a faster way to narrow down the results.

Single term queries: If you enter a single term, the search (Focused Results) will find documents that have a statement that connects the search term to other concepts. This enables you to find the most important connections for the search term.

Two term queries: If you search for two objects, such as "protein1 protein2", the focused search will find documents that connect the two objects by an action, such as "protein1 regulates protein2", and the search will find documents that connect the two objects indirectly, such as "processA affects protein1 and protein2". If you search for an object and an action, such as "ethanol causes", you will find documents that have a specific statement about ethanol causing something.

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Use a Power Term® class to explicitly find the "what" that ties your two terms together. For example, "ethanol causes $Diseases" to find what diseases ethanol causes.

Three term queries: Extending the approach as described above, you can see that a query consisting of "object1 action object2" will allow you to find the documents that support that specific connection.

Complex Boolean queries: You do not need to create complicated Boolean queries to cover all the various names for objects or to deal with various stemmed forms - all that is handled automatically for you. Just use the terms you are familiar with. BioAI™ does not currently support queries such as "protein1 OR protein2 bind to protein3 AND protein4".

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Capitalization
Use proper capitalization in your queries so that you can focus on a capitalized term - for example, finding "AIDS" (the disease) and instead of "aids" (the action). You will find this to be of particular value where a gene symbol (e.g., MAID) is also an English word.

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Power Term® Queries
When formulating a query, you may want to find members of a class of objects. For example, instead of the broad query "protein apoptosis", you may want to know about specific proteins. To enable queries of this type, BioAI™ supports a number of Power Term® queries that represent an entire class of objects. The most important characteristic of a Power Term® class is that it focuses only on the member of the class, rather than the name itself (or its synonyms), which is often too broadly used in the literature to be useful. Moreover, when you use a Power Term® query, then all members of that class found to be connected to your other query terms will be listed in the "Key Concepts" filter section.

Example The Power Term® class $Proteins means any protein, but not the word "protein" or "proteins", allowing you to focus on what is meaningful rather than getting back long lists of results that contain the non-specific term "protein".

The query "$Proteins apoptosis" will find documents that refer to specific proteins being involved in apoptosis. And, a list of proteins involved in apoptosis will be presented in the Key Concepts filter.

The most commonly used Power Term® queries; can be found in the link directly under the main search box. In the window that opens from this link, you can click on a Power Term® query to add it to your search. The full list of Power Term® queries is available here.

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You can copy all the Power Term® class members relevant to your query directly from the Key Concept filter. If necessary, click the "More »" link to expand the section. Then, use your mouse to select the entire list and copy this to your clipboard.

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Searching for Chemicals
In searching for chemical entities, long names can be difficult to enter. So all the BioAI™ products offer you the choice of searching by identifier number. A variety of ID or registry numbers are recognized, including CAS numbers. Not all IDs or registry numbers are available for all substances. The various identification numbers are copyright of their respective providers.

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Searches that Require Special Handling
Some terms are easily confused due to multiple meanings. If you are not finding the results you expect, it may help to use the correct capitalization (where appropriate). In some cases, you may want to try alternative names for what you are looking for.

Example Elemental Lead: There is not usually sufficient context in a short query to understand what meaning of "lead" you intend. So, if you are looking for documents about Elemental Lead, you should use one of the following search terms: plumbum, elemental lead, or Pb (the latter being case-sensitive). An ID or registry number will also work. This will make it clear what your search means.

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Search Suggestions
As you enter your search terms, you will see search suggestions displayed. These suggestions are based on actual content; they are not based on what others have searched for.

The search suggestions consist initially of a possible entity (protein, chemical, disease, etc.) that matches what you have typed so far. For each entity, there is an icon (e.g., disease icon) representing the type of object. If you position your cursor over the icon, you will see the name of the object type. Following is an example.
Search Suggestions
In the above example, the cursor on the icon for "canine" shows this is an Organism. Next to the entity type icon is a green color block that indicates the relative frequency. Brighter and larger means frequent; darker and smaller means less frequent. When the search suggestion is ambiguous or is constructed from common terms, the type icon and frequency color will not display.

If your search consists of an entity followed by "and", as you type the next characters the search suggestion shows possible additional entities for you to choose. The type icon and frequency color then apply to the second entity.

To execute the search suggestion, you can click on the entry or use the arrow keys to select the suggested search and then hit Enter.

To use the search suggestion as part of your search, if you use your mouse to click a suggestion, that search will be immediately executed.

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If you use the keyboard's arrow keys (↓ and ↑) to highlight a suggestion, that suggestion then populates the search box and you can keep typing to complete your query. Select a suggestion using the arrow keys and then type "and"; a new list of suggestions will then be shown as you type.

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Search Using an Author Name
When looking for documents that are by a specific author, you can simply add the author's name to the Author search box. The Author search box is the second entry area in the search panel.

If you also have a query in the main search box, adding one or more authors to the Author search box will limit the results to documents that include those authors. If you have no query in the main search box, an author-only query will find all the documents with the author(s), but no Relevant Statements will be found; hence, the list of documents will be shown on the Broader Results tab.

To enter an author, start typing the author's name in the Author box. After you enter three characters, a drop-down list appears to allow you to pick the author from the list. Initially, the more prolific authors that match your typing are shown, so you may have to continue typing to have the drop-down list display the author you want. You may also type the name directly, without using the drop-down list.

To add additional authors, separate each author by a comma (for example, Simpson LA, Johnson JJ). When searching for multiple authors, documents that contain all of the names listed will be found. All searches, including those for just an Author Name are executed by clicking the Search button in the main search box.

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Search Using a Publication Source
When looking for documents that are in a specific journal, you can simply add the journal's name to the Journal search box. The Journal search box is the third entry area in the search panel.

If you also have a query in the main search box, adding one or more journals will limit the results to documents that are from the selected journal(s). If you have no query in the main search box, a journal-only query will find all the documents from the journal(s). Since no text terms were included, the list of documents will be shown on the Broader Results tab.

To enter an journal, start typing the journal's title in the Journal box. You can use the full title, such as "Journal of Bacteriology" or an abbreviated form, such as "J Bact". After you enter three characters, a drop-down list appears to allow you to pick the journal from the list. You may have to keep typing to find the specific journal of interest.

To add additional journals, separate each entry with a comma. When searching for multiple journals, documents that contain any of the journals listed will be found. All searches, including those for just a Journal Name are executed by clicking the Search button in the main search box.

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Search for only a Journal name, then Sort by Date (or use the "Last 30 days" Publication Date filter to see what is new in your favorite journal.

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Search Using an Affiliation
When looking for documents that are from a specific organization, just enter the organization's name to the Affiliation search box. The Affiliation search box is the third entry area in the search panel.

If you also have a query in the main search box, adding one or more affiliations will limit the results to documents that are from the selected organization(s). If you have no query in the main search box, an affiliation-only query will find all the documents from the organization(s), but no Relevant Statements will be found, only a list of documents shown on the Broader Results tab.

To enter an affiliation, start typing the organization's name in the Affiliation box. After you enter three characters, a drop-down list appears to allow you to pick the organization from the list.

To add additional organizations, separate each entry with a comma. When searching for multiple journals, documents that contain all of the organizations listed will be found. As such, this is very useful for finding collaborations. All searches, including those for just an Affiliation are executed by clicking the Search button in the main search box.

Remember that departments and organizations change names, authors change institutions, and authors from the same institutions may use different affiliation name forms. The BioAI™ platform strives to find as many variations as possible. If you find that we're missing something, please contact us.

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For patents (Qinsight), the Affiliation includes the Assignee.

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Search Using Patent-specific Fields (Qinsight)
Qinsight provides a number of patent-specific search fields. These can be accessed by clicking the "Show Additional Patent Search Options +" link at the bottom of the search panel. View the hint information next to each search box for further details. All searches, including those using the patent search options are executed by clicking the Search button in the main search box.

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Results - Help

Understanding the Results
Focused Results: The focused results are documents that determined by the BioAI™ artificial intelligence engine to be relevant to your query. That assessment of relevance is made by examining the informative text (excluding noisy information such as references) across the entire document. To help you see how the results are indeed relevant to your query, one or more Relevant Statements tying your search terms together in a meaningful way are displayed.

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When your query contains only one term: BioAI™ finds occurrences of that term, with a preference for places where (a) the term is used alone such as a section heading (implying significance) and (b) places where the term is used in conjunction with other known entities (implying importance).

When your query contains multiple terms: BioAI™ finds statements where all of the query terms are used together. This may be in a direct subject-verb-object relationship or in an indirect connection. For example, if your query is for the two proteins p53 and Sp1, a direct connection would be "Sp1 overexpression induced p53 translocation from nucleus to cytosol" and an indirect connection would be "Pdcd4 affects the activities of several transcription factors, such as c-Jun, Sp1, Twist1, p53 and NF-kB" - in this case implying a common regulatory pathway.

Relevant Statements may be from the document's Title, Abstract, Body (Introduction, Methods, Results, Discussion, Figure Legends, or Tables) - collectively, we refer to these sections as the Informative Text. Relevant Statements are NOT derived from Non-informative Text including references, acknowledgments, or metadata such as MeSH terms (these are not created by the author).

The Relevant Statements, presented on the Focused Results tab, provide rapid access to the critical facts in the literature that are relevant to your query. Up to five such Relevant Statements (the five most relevant) will be shown for each document. By default, one Relevant Statement will be displayed, but you can see the others (up to 5 total) by clicking "More Relevant Statements" (see the red oval in the following figure).

Result showing Relevant Statement Controls

If you so desire, all the Relevant Statements for a result set can be expanded simultaneously by clicking the "Show All Relevant Statements" link at the top of the Results section (see the blue square in the above figure).

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If the only Relevant Statement is in the document title, this will not be repeated below the result.

Broader Results: BioAI™ also searches for documents based on keywords, giving you a broader set of documents. That is, if a document contains all of your search terms (or their synonyms), that document will be listed - even if those search terms are not used together in any meaningful way (for example, being in different sections of the document). To access the Broader Results, click the "Broader Results" tab.

Search Results: For some searches, such as for an Author name only, there are no Focused Results and the results tab is labeled "Search Results".

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Results Display
Author List: The document authors are provided directly under the result title, with the first author shown. If there is more than one author, there will be a "More Authors »" link; click this to show all the authors. When available, the author's affiliation will be shown next to the name.

Example Result Display

Document Source: The document source (for example, the journal name) is provided under the author(s). Journal names are displayed in an abbreviated format; mouse over the title to view a tool tip will with the full title.

Publication Date: The publication year is displayed following the Document Source. Mouse over the date and a tooltip will show the full date, as provided by the document's publisher. If no tool tip appears, the publisher only provided a year for the publication date.

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For patents (grants and applications), the date used is the date the grant or application was published. The Filing Date is available in the Details section for each patent results display.

Context and Highlighting: For Focused Results, the Relevant Statement(s) matching your query will be displayed to provide the context. For Broader Results, one sentence from the document containing all of your query terms will be shown. If no sentence in the Informative Text of the document is found with all of your query terms, a sentence containing one or more query terms will be shown, along with an indication of where in the document the other query term(s) were found. For both Focused and Broader Results, query terms are italicized and highlighted in yellow.

View Abstract: To view the full abstract for any result, simply click on "Show Abstract »"; this link is on the Source (Date) line. To close the abstract, click on "« Hide Abstract". When the abstract is shown, any Relevant Statements are temporarily hidden until the abstract is closed.

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Accessing the Document
To view the original document click on the document title.

For direct access to the PDF version of the document, when available, click the PDF icon that follows the title.

For Patent Grants and Applications (Qinsight only), the PDF link takes you to a site that displays the PDF. You then need to download this. In Firefox, just click the download icon at the top. In Safari and Internet Explorer, hover your mouse over the page and then click the Save icon. In Chrome, right-click on the page and then choose "Save As".

To access full-text documents through your organization's subscriptions, click the My Library link that follows the title. Note, this is only available if your organization connects its holdings to our applications (free and easy). Ask your librarian to contact Quertle.

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Sorting
To enable you to find the most relevant documents faster, the results are initially presented in order of relevance to your query. To sort the results by date, simply click the "Sort by Date" link. This control is on the upper right, just above the first result entry. The results will now be sorted by date (most recent first). To return to relevance-based order, click the link at the top that now displays "Sort by Relevance". Your preferred sort order is remembered and applied to subsequent searches, until you change it.

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How BioAI™ defines relevance: Several parameters are used to determine relevance. The biggest contributor to this relevance measure is how many times the author has tied your search terms together in a meaningful way. The location where you search terms are tied together also matters, with Titles having the highest weight.

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Exporting
On the Results page, you can select and export references for use in bibliographic management software.

To select a result for export, simply click the checkbox at the beginning of that reference. The remaining Export controls are located on the left side just above the first result on the page. To select all results on the current page, click the Select icon. To clear all selections on the current page, click the Clear icon. To clear all selections from the current search, no matter what page they are on, click the Clear All icon. You do not have to mark any references if you want to export all of the results; you will have this option in the Export dialog.

To export, click Export at the top of the results list. You have the option to export all results (up to a maximum of 1000) or just the ones you have selected. Note that the First 1000 is sensitive to the sort order you have chosen (by relevance or by date). You also have the choice of export format.
  • Bibliographic Management Software (RIS) is a tag-delimited format used by most bibliographic software packages. Choose this if you want to import the results into your bibliographic software.
  • Spreadsheet (CVS) is a standard comma-separated value file that can be opened by spreadsheet software.
When you click Export, your bibliographic management software may launch automatically, if your package supports this function.

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Filters - Help

Refining Results
Refining your results is easy using a set of filters conveniently located left side of the results page. As you apply a filter, the Applied Filters section at the top left will update to show "breadcrumbs" for the filter(s) that have been applied. These breadcrumbs allow you to remove any or all of the filters easily.

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Published Within (Publication Date)
To limit the results to a specific period of time, simply click on the desired time frame and the results will update accordingly.

For Qinsight only, you also have the option of defining a Custom Date Range. You may enter information in all the fields, or you may choose to leave certain fields blank. For example:
     "2013 to 2014" would cover 2013-01-01 to 2014-12-31

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Publication Type
To limit the results to a specific type of publication, simply click the box next to the desired type(s). Click "More »" to show additional publication types, if desired. If you select more than one publication type, the filter will limit results to any of the selected types.

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Note that publications may have more than one Publication Type. For example, an article could be a Journal Article, a Clinical Trial, and a Twin Study.

Also note that many new publications are available on our site prior to the type(s) being assigned. Once the Publication Type is assigned by the National Library of Medicine, our records will update.

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Also Containing (Focus on Results with Specified Terms)
Use the "Also Containing" filter to essentially add a term to your query. The results will be narrowed down to documents that contain the additional term anywhere in the text, in the MeSH terms, or in the Chemical or Gene lists. After you apply an "Also Containing" filter, the term used will be bolded in the results display. For example, if you searched for "diabetes treatment" and then applied "patient" in the Also Containing filter, you would end up with only the documents that had "diabetes" and "treatment" in at least one Relevant Statement PLUS the term "patient" anywhere in the document.

For Qinsight: For Focused results, you have an option for the additional term(s) to be found specifically "In Relevant Statements". This would limit your results to documents that contain your term(s) in the Relevant Statements from your previous set of results. For example, if you searched for "diabetes treatment" and then applied "patient" in the Also Containing filter using the "In Relevant Statements" option, you would end up with only the documents that had "diabetes", "treatment", AND "patient" in at least one Relevant Statement.

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Not Containing (Exclude Results with Specified Terms)
Use the "Not Containing" filter to exclude documents that contain the specified term(s) anywhere in the document (text, MeSH terms, or the Chemical or Gene lists). For example, if you search for "diabetes treatment" and then add "mouse" in the Not Containing filter, you would end up with only the documents that had "diabetes" and "treatment" in at least one Relevant Statement, BUT NOT the term "mouse" anywhere in the document.

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When applying the Not Containing filter, you eliminate all documents that include the additional term(s), even if a different topic of interest was present. For example, if you do a Not Containing filter for "mouse" in order to focus on humans, the updated results would exclude the documents that mentioned both. In some cases, this may be the desired effect, but you should be aware of the possible consequences.

For Qinsight: For Focused results, you have an option for the Not Containing term(s) to be found "In Relevant Statements". This would limit your results to documents that do not contain your term(s) in the Relevant Statements from your previous set of results. For example, if you searched for "diabetes treatment" and then applied "mouse" in the Not Containing filter using the "In Relevant Statements" option, you would end up with only the documents that had "diabetes" AND "treatment", BUT NOT "mouse" in ALL of the Relevant Statements.

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Negative Statements (Focus on or Exclude Terms) (Qinsight only)
This filter allows you to focus on or exclude Relevant Statements that may imply a negative, such as "A does not cause B".

The "Exclude Negatives" filter allows you to limit the current results to those that have a positive connotation. Note that removing a negative Relevant Statement from a result that also contains positive statements will not remove the document from the result list. Only the Relevant Statement will not be displayed.

Example Consider the following two Relevant Statements:
More importantly, patients with AML and MDS with BCOR mutations exhibit poor prognosis.

Mutations in BCOR were not detected in 131 AML cases having various cytogenetic abnormalities

Both sentences connect the BCOR gene with Acute myeloid leukemia (AML). Applying the "Exclude Negatives" filter would remove the second Relevant Statement, making it easier for you to focus on the positive statements.

The "Show Only Negatives" filter is used to refine the results to those that specifically include a negative connotation. A result containing positive statements may not be removed if it also contains negative Relevant Statements; only the Relevant Statement would be removed. After you apply the "Show Only Negatives" filter, the terms that imply the negative association will be bold and red in the results display.

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Key Concepts
The "Key Concepts" filter shows concepts relevant to your query (not just anywhere in the results document) with the most frequent within each section at the top. Click on any of these concepts to limit the results to those that include that concept. You may select more than one Key Concept for additional filtering and you can remove any one by clicking the concept again or by removing it from the Applied Filters section. The term you click on will be bold in the results display.

For all subscriptions except Qinsight, the Key Concepts do not update with filtering. This maintains the original set of Key Concepts for filtering.

For Qinsight, you have the option to have the Key Concepts remain fixed when filters are applied, or to update with filtering. The latter option can be very useful when combined with the Visual Analytics.

The Key Concepts are broken out into sections:
Power Term® Membership: For each Power Term® class used in your query, the "Key Concepts" filter will display a section for that class. In this section, the members of the class that were found in Relevant Statements will be displayed, in order of their importance. "Automatic" classes, such as "leukemia" (all forms of leukemia) will also be separated into concept groups. The full list of Power Term® queries includes all the Power Term® queries you can use.

General Concepts: This section will identify other key concepts, even if they do not belong to a defined class. Such General Concepts are automatically discovered by BioAI™ even if they are not previously known.

Actions: The section labeled Actions contain concepts related to actions that are associated with your query. These actions are generally listed by the noun form; the actual term used in the Relevant Statements may be any part of speech. This section may not be shown if your search specified an action.

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Visual Analytics - Help

Concept Cloud (For Qinsight only)
The Key Concepts essentially summarize the concepts in the documents that are relevant to your query. To launch the Concept Cloud, click
     Concept Cloud Button
The visualization will open in a pop-up window.

The Concept Cloud presents all the Key Concepts in a single visualization so that you can assess the relative contribution of each concept across all of the individual Key Concept sections. Larger text means the concept was connected to your query more frequently in the results set than terms with small text. Each Concept Cloud provides a legend at the top, so that you can see which category each concept belongs to.

In the Concept Cloud, if you click on any concept, the documents containing that concept in a meaningful connection with your query will be shown in the results list. You can treat this like any other filter and remove the selection from the Applied Filters section or combine it with other filters.

To export the data underlying the Concept Cloud, click
     Export Data
This will create a tab-delimited file with all the Key Concepts along with the number of documents in the results that use that concept in a meaningful connection with your query. You can then use these data for other analytical purposes.

To save the Concept Cloud as an image, click
     Save Image
This will create a PNG (Portable Network Graphics) file with the image. Or, you can simply create a screenshot of the pop-up window. You can then use the image for documentation or reporting purposes.

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Concept Trends (For Qinsight only)
The frequency with which Key Concepts appear is only part of the story. It is also of interest to determine whether a concept is becoming more important, or is mentioned a lesser amount over time. The Concept Trends visualization provides that insight. To launch the Concept Trends visualization, click
     Concept Trends Button
The visualization will open in a pop-up window.

The Concept Trends visualization shows each Key Concept as a bubble, with the size of the bubble indicating the number of documents in the current results set where the related Key Concept was found. The bubbles are color-coded by Key Concept category and a legend is provided at the top.

Each bubble also has a border which is an indication of trend. If a concept (as related to your query) is becoming more important (increasing trend), that bubble will have a red border. If a concept (as related to your query) is becoming less important (waning trend), that bubble will have a blue border. Otherwise, the border will be gray.

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Concept trends are discovered using documents from the last year. As such, if you have applied a Publication Date filter that does not cover the past year, the trend discovery process is skipped and all borders will be gray.

To export the data underlying the Concept Trend Visualization, click
     Export Data
This will create a tab-delimited file with all the Key Concepts along with the number of documents in the results that use that concept in a meaningful connection with your query. You can then use these data for other analytical purposes. The trend information is not exported.

To save the Concept Trend Visualization as an image, click
     Save Image
This will create a PNG (Portable Network Graphics) file with the image. Or, you can simply create a screenshot of the pop-up window. You can then use the image for documentation or reporting purposes.

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Concept Connections (For Qinsight only)
When you use a Power Term® class in your query, you are presented a list of the members of that class relevant to your query. If you are interested to know if any the members of the class are used together in a meaningful connection (and still relevant to your query), the Concept Connections visualization can provide insight.

The Concept Connections visualization provides a matrix indicating how often all relevant Power Term® members occur together. The more intense color implies more connection between the concepts.

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The Concept Connections visualization is much more than simple co-occurrences, which can often be misleading. The BioAI™ artificial intelligence is able to discover meaningful connections between any of the Power Term® members. This provides substantial insight about interactions among the Power Term® members.

To launch the Concept Connections visualization, click
     Concept Cloud Button
The visualization will open in a pop-up window.

In the Concept Connections visualization, more intense color implies a stronger connection between the concepts. Initially, the visualization will be presented in cluster order, which emphasizes the connectivity. You also have options for frequency and alphabetical order.

In the Concept Connections visualization, if you click on a cell, the documents containing that pair of concepts will be shown in the results list. This is equivalent to selecting both concepts in the Key Concepts filter. You can treat this like any other filter and remove the selection from the Applied Filters section or combine it with other filters.

To export the data underlying the Concept Connections visualization, click
     Export Data
This will create a comma-separated value (CSV) file with all the matrix values. You can then use these data for other analytical purposes.

To save the concept Connections visualization as an image, click
     Save Image
This will create a PNG (Portable Network Graphics) file with the image. Or, you can simply create a screenshot of the pop-up window. You can then use the image for documentation or reporting purposes.

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My Space - Help

Saved Searches
You can save your current search - along with all the currently applied filters. This makes it easy to re-run the query and provides an optional automatic email Alert when new documents are added.

Saving a Search: On the Results page, you will see a Active Star = Save Search Save Search+Filters link at the top right of the results. Clicking this link will save the current search and all currently applied filters. If you apply a different set of filters on the same search, that can be saved separately. If the current search and applied filters have already been saved, the link will display Inactive Star = Search Already Saved Search Saved in My Space.

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Your Saved Searches are encrypted on the server to protect your privacy.

Re-running a Saved Search: Go to your My Space page and, if necessary, click the Saved Searches tab. For each Saved Search, you will see all of the search and filter parameters. To run a saved search, simply click Run Saved Search Button.

New Document Alerts: To get a weekly Alert for a specific Saved Search, click the checkbox in the Alert column. You will receive an email each week alerting you to any new documents that meet your search plus filter criteria. If you request alerts for multiple searches, all the Alerts will be bundled in a single email. You may stop Alerts at any time by unchecking the desired Saved Searches. At this time you cannot change the frequency of the Alerts.

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Saved Articles
You can save a specific result to your My Space Saved Articles. When you save the document, you have the option of adding private notes.

Saving an Article: On the Results page, click the Save icon (Save Article) located to the left of the result entry. In the window that opens, you may enter a note you want to save with the article.

Viewing a Saved Article: Go to your My Space page (the link is at the top right of the search panel) and click the Saved Articles tab. The Saved Articles are shown with the most recently saved article at the top. For each article, the display is similar to that on the results page, so you have easy access to the original document and you can view the Abstract and additional Relevant Statements (if applicable).

Adding or Modifying Private Notes: Each Saved Article has a notes section located underneath the article information. You may edit the content of the notes box by clicking inside the box. You may add additional notes, or delete existing notes. When you are done, just click outside the box. Your notes associated with a Saved Article are private. These are encrypted on the server and they are not shared with others when you start a Journal Club.

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Your Saved Articles and private notes are encrypted on the server to protect your privacy. Private notes are not shared within Journal Clubs.

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Journal Clubs
You can discuss a specific article in a Journal Club. Journal Club discussions are private. Only invited colleagues can participate and all discussion comments are encrypted on the server.

Starting a Journal Club: Journal Clubs are started from Saved Articles, so be sure to save the article to your Saved Article space first. The other participants do not have to have the same article saved. On your Saved Articles page, click the Start Journal Club icon. (The gray color indicates the Journal Club is inactive.) In the dialog that opens, simply enter the email addresses for the people you want to participate in the Journal Club discussion.

Viewing your Journal Club List: The Journal Clubs you start are listed on your Journal Clubs My Space page in the "Journal Clubs Started by Myself" section. The Journal Clubs you were invited to join are listed in the "Journal Clubs Started by Others" section.

Viewing a Journal Club Discussion: To view an active Journal Club, on your My Space Journal Club page, click the View the Discussion icon icon. A new window or tab opens showing the Journal Club. The article is shown at the top, with the same functional controls as on a Results page.

Adding a Comment to a Journal Club Discussion: To start or add to the Journal Club discussion, click the Note icon that appears just under the article presentation. In the dialog that opens, enter you comments. They will appear on the page momentarily.

Adding New Member to a Journal Club Discussion: To add new people to an existing Journal Club discussion, click the "Invite new discussants" link in the Invitees box on the right-hand side of the page.

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All Journal Club Discussions are encrypted on the server to protect the privacy of your discussion group.

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Your Preferences
To set your My Space preferences, click on Your Space at the top right of the search area. Your preferences will be listed on the Preferences tab. Currently, the only preference is how many results to show on each page.

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Your Profile
To change your profile, click on Your Space at the top right of the search area. Your profile will be listed on the My Profile tab. You may update any of the fields, including your email address.

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Your Account
To change your subscription account settings, profile, click on Your Space at the top right of the search area. Your account information will be listed on the My Account tab.

Your Version: Your subscription version is shown at the top of this section. To change to a different version (you can review the product information on the Quertle.com website, on your My Account page, click the "Change" link that follows Your Version.

Your Renewal Period: Your renewal period is shown on the second line. To change from a Monthly subscription to a Yearly Subscription, click the "Change" link that follows Your Renewal Period.

Automatic Renewal: To ensure uninterrupted access, your subscription is initially set for automatic renewal. To cancel the next renewal, click "Cancel Renewal". Your access will continue through the current period and then be canceled.

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Registration and Subscriptions - Help

Registration
All users must register for an account.

If you are an individual user from an academic or non-profit organization (including government agencies) or you are a healthcare provided from a hospital or private practice, you will find product information, pricing, and registration links at Quertle.com.

If you are from an organization with a site license, you should see
      a Happy News message with a Register link
where "My Organization" will be replaced by the actual name of your organization. Click the "register" link and complete the form. You will not incur any charges.

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Subscriptions
For information about the different products available by subscription, please visit Quertle.com

Renewal Period: After you have registered, you will need to choose whether you want a monthly subscription or a yearly. There are significant savings with yearly subscriptions.

Changing Your Subscription: To make any changes to your current subscription, go to your My Space page using the link at the top right of the Search Panel, then click the My Account tab on the far right. On that page, you can change the version you are subscribed to, the renewal period, and the automatic renewals.

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Automatic Renewals
To ensure uninterrupted service, subscriptions automatically renew. If you want to cancel the automatic renewal, on your My Space My Account page, click Cancel Renewal on the Automatic Renewal line.

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Changing your Password
To change your login password, login, tap/click on Your Space in the upper right of the search area and then tap/click on My Profile tab. At the bottom of the profile form, enter your new password and confirm, then click Save.

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Searches - FAQ

What content is covered?
The full list of content covered by Quertle® products is available here. Currently, about 40 million documents from about 26 thousand journals plus patents, and many other sources. More than 10 million of the documents are full-text for in-depth searching. Some of the full-text journal articles are obtained from PubMed Central's Open Access Subset. Not all sources are available for all subscription levels. Custom solutions may also contain your licensed content or even in-house documents.

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How can I get assistance or training from a REAL person?
Contact us to ask a question or to find out about free training sessions.

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How should queries be written?
Searches on are best constructed by focusing on a core concept, saving other qualifiers such as "in mice" or "review" as filters. For example, you could write "aspirin treats headache" to find all documents about that subject. You can also use a Power Term® class for the subject or object as in "$Chemicals treat headaches?" (to find documents on chemicals that treat headaches) or "aspirin treats $Diseases?" (to find documents on what diseases aspirin treats). Or, you can simply enter one or more terms. See the Help section above for details.

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Are queries case-sensitive?
For most terms, case does not matter. Some terms, however, have very different meanings when used in a particular case. For example, consider "NO" (nitric oxide) and "no" (negative), or "AIDS" (disease) and "aids" (helps). In these situations, you should use proper capitalization.

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Can I enter a query with Boolean logic (AND, OR, or NOT)?
No. Since the underlying BioAI™ artificial intelligence engine matches your query to the points made by the author(s), you should not include Boolean operators. It is better to add additional terms (AND) using the Also Containing filter or remove terms (NOT) using the Not Containing filter. And, remember, BioAI™ automatically finds all synonyms and related concepts so complicated Boolean is not necessary.

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Can I look for a specific phrase using double quotes?
No. BioAI™ conceptualizes your query to give the most relevant results. BioAI™ takes input such as pinocytosis inhibition and understands when it has a conceptual match, such as fluid-phase endocytosis was inhibited by and so on. Thus, forcing a search for specific phrases is counterproductive and not supported. BioAI™ also has learned about most things biological and chemical and will automatically recognize phrasal entities, such as cell cycle. If you think we aren't understanding something, please let us know.

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What Power Term® classes can I use?
A Power Term® class is used to represent a class of entities, such as $Diseases (representing all diseases), not the generic term "disease". The most commonly used Power Term® queries can be found in the Power Term® class pop-up window. This can be accessed by clicking the link below the Search box. You can also view the full list of Power Term® class. If there is a Power Term® class you think should be included, please let us know.

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Can I create my own Power Term® class?
No. You cannot simply add a $ at the beginning of a query term to make it a Power Term® class. If you want your term included, let us know. We trained the BioAI engine for all the other Power Term® classes and can usually do the same for you.

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What does the $ mean?
The $ signifies that the search will be for the members of that Power Term® class BUT NOT for the term itself. For example, the word "disease" is very common in the literature and it is not always helpful to search for that. Instead, if you want to find actual diseases - but not "disease", "syndrome", etc. - then the Power Term® $Disease is what you would use.

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Can a Power Term® class be typed into the query or must they be picked from the pop-up?
Yes. The pop-up list is a convenient way to enter a Power Term® class, but you can also enter a Power Term® class by typing it directly in the Search box. But be sure to check the full list of Power Term® classes periodically, as new Power Term® classes are frequently added.

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Are MeSH terms used?
The Focused Results are looking at text written by the author for Relevant Statements that tie your search terms together. MeSH terms are not written by the author, nor do they necessarily imply a relationship. Thus, for Focused Results, the search does not use MeSH.

Example An article on adverse effects of drugs states
    "doxorubicin causes congestive heart failure"
and separately
    "dofetilide causes long QT"

These two statements do not imply doxorubicin causes long QT even though both would be MeSH terms. The BioAI™ artificial intelligence engine uses much smarter, modern methods.

Having said that, we note that MeSH terms can be extremely useful. So, once the documents are found to contain author-written Relevant Statements that match your search terms, drilling down using the Also Containing filter does use MeSH. (Note: for Qinsight users, this would be Also Containing with the "Anywhere" option.) Similarly for the Not Containing filter.

MeSH terms are also used for the Broader Results. These results relax the requirement for the search terms to be used in a meaningful connection, looking in all the informative sections of the document (text as well as the MeSH, chemical, and gene lists).

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How do I search for an author?
Unlike some other sites, you should not enter the author(s) of interest in the main Search Box unless you are specifically looking for Relevant Statements written about a person. Please type in the author(s) of interest in the Author Search box. As you type in an author's name, a list shows some possible matches. As you type more, the list will update accordingly. You do not have to actually pick from the suggestion list if you prefer to type the entire name. You can search for multiple authors by entering more names in the Author Search box, each separated by a comma. If more than one author is entered, the results must contain all of the names.

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What if I don't see the author I am looking for in the suggestion list?
Keep typing. The list cannot show all possible matches (e.g., if you are looking for "Smith") and shows the more prolific authors that match what you have typed so far. As you type further, you should see who you're looking for.

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How do I search for a specific journal?
To limit your query results to those from a specific journal, enter the journal name in the Journal Search box. As you type in a journal name, a list shows some possible matches. As you type more, the list will update accordingly. You do not have to actually pick from the suggestion list if you prefer to type the entire name. You can search for multiple journals by entering more names in the Journal Search box, each separated by a comma. When entering multiple journals, the results will be for any of the entered publications.

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What if I want to search by author or journal without any other terms?
No problem. Just enter the author(s) and/or the journal(s) and leave the main Search box empty. In this case, there are no Focused Results. But you can further filter to a topic of interest simply by adding a term in the "Also Containing" filter found on the left side of the results page.

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What if I want to limit results to those by authors from a specific organization?
You can enter the Affiliation in its separate search box (to avoid finding statements about an institution).

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For Qinsight, the Affiliation search box also applies to patent assignees.

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How do I limit the dates being searched or apply other filters?
The date, publication type, and term-based filters are found directly on the results page. Do your query first and then limit the results as desired afterward.

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Results - FAQ

What's the difference between Focused Results and Broader Results?
Focused Results are documents found by the BioAI™ artificial intelligence engine to that contain your search terms connected in a meaningful way. This is much more specific than just having the terms found in the same document and are based on the context and implication of the text. The result is a set of documents that are highly focused on your query.

Broader Results are documents found by doing a keyword search for your query terms - and their synonyms - regardless of whether the words are used within the same context, or even within the same section of the document.

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Why are there fewer Focused Results than Broader Results?
In most cases you will find fewer Focused Results than Broader Results. When searching for multiple terms, the Focused Results show documents that use the multiple terms together in a meaningful way, whereas the Broader search will find more documents because the terms do not have to be linked.

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What is the highlighting?
The terms and phrases highlighted in yellow are your query term(s), their synonyms, or members of their class. If you have added an "Also containing" filter or have clicked on a Key Concept, those terms will be in bold. If you prefer not to have the highlighting shown, click "Turn Highlighting Off" at the top of the results. To turn it back on, click "Turn Highlighting On". If the matching term occurs in the MeSH terms, the Chemical list, or in another part of the body of the document, that match will be presented at the bottom of the result listing.

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Why are some terms italicized?
The BioAI™ engine automatically discovers abbreviations on a document-by-document basis. When text displayed from a document contains a recognized abbreviation, that abbreviation is italicized.

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How are the results ordered?
Results are initially ordered according to what is most relevant to your search.

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Can I reorder by date?
Yes. Simply click on "Sort by Date" at the top of the results list. The results will now sort by date, most recent first. To go back to relevance sorting, just click on "Sort by Relevance". You choice of sort order is remembered from search to search.

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What does the date "Epub" mean?
Many publishers submit electronic versions of accepted articles prior to their actual publication. These articles have a print publication date sometime in the future. All such future dates are shown as "Epub" (Electronic publication ahead of print).

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Can I save or export my list of documents?
You can export selected results or all of the results (up to 50000) directly to your bibliographic manager software or to a file. See Help for guidance on using the export feature.

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Filters - FAQ

What types of filters are available?
  1. Published Within: Documents can be filtered by date to show only those published within defined time intervals, such as the previous 30 days. For Qinsight, there is an additional Custom Range where you can define precisely the date range you want.

  2. Publication Type: Documents can be filtered to show specific types of publications. Simply click on the publication type of interest. Note that clicking more than one publication type will filter the results to ANY of the selected types. To undo your choice(s), simply delete the Publication Type from the Applied Filters or click the individual entry in the Publication Type filter. Let us know what other publication types you would like to be able to filter by.

  3. Also Containing: You can type in additional words to be searched for in the current results set by typing into the "Also Containing" text box, then click Search or hit Enter. This will filter documents to those that contain the additional terms anywhere within the informative text - title, abstract, body (for full-text), MeSH terms, or Chemical list. The "Also Containing" filter always looks for the term you enter, all of its inflected forms (such as plurals), all of its synonyms, and all of its "children" in the ontology (for example, "rodent" will find "mice", "rats", and so on). For Qinsight: You have an additional option to require the Also Containing term(s) to be in the Relevant Statements that were found by the initial search.

  4. Not Containing: You can enter additional term(s) that you do not want in the search results. Just enter the terms into the "Not Containing" text box, then click Search or hit Enter. This will filter documents to those that do NOT contain the additional terms anywhere within the informative text - title, abstract, body (for full-text), MeSH terms, or Chemical list. The "Not Containing" filter always looks for the term you enter, all of its inflected forms (such as plurals), all of its synonyms, and all of its "children" in the ontology (for example, "rodent" will find "mice", "rats", and so on). For Qinsight: You have an additional option to require the NOT Containing term(s) to be in the Relevant Statements, thus removing those Relevant Statements from contributing to whether the article remains on the results list or not.

  5. Negative Statements: (Qinsight only) This filter allows you to focus on or exclude Relevant Statements that may imply a negative, such as "A does not cause B".

  6. Key Concepts: One of the most useful aspects of the filter set is the ability to limit documents to those relevant to a concept of interest. Quetzal® automatically identifies key concepts in the initial results set (based on the search term(s) entered into the main search box) that are relevant to your query. When you have used a Power Term® class, the Key Concepts filter lists the members of that Power Term® class that were found in Relevant Statements matching your query. Click on any term in the "Key Concepts" section to show only those documents containing the specific results of interest. To undo the filtering, just delete the term in the Applied Filters section.
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How do I use the Applied Filters?
When you apply a filter, a "breadcrumb" is left in the Applied Filters. You can eliminate any (not just the last) filter by clicking the corresponding X or by clicking the entry again in the filter section. You can also go back to a prior set of results by clicking on a breadcrumb link, which removes all filters below it. To remove all filters, click the X following the Applied Filters label.

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Can I apply more than one "Key Concept" filter?
Yes. You may select any number of Key Concepts (one at a time) and combine those filters with any number of other filters.

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I think a certain term should be on the "Key Concepts" list, but it isn't. Why?
The top concepts (or members of a Power Term® class) are defined from the most relevant documents and are limited to the most 100 important concepts in each category. The term you are looking for is likely just less relevant. In this case, you should use the Also Containing filter to limit the results to the term you are interested in.

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Visual Analytics - FAQ

How is the Concept Cloud Calculated? (For Qinsight only)
The Concept Cloud shows all the Key Concepts (the concepts in the results documents that are specifically related to your query). The size of each concept reflects the number of documents in results that tied that concept to your query in a meaningful way. As such, the Concept Cloud is essentially a summary of what the results set is all about.

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What does the Concept Trends Visualization Mean? (For Qinsight only)
The Concept Trends visualization is a spiral clustering of the Key Concepts. The size of each bubble represents the number of documents where that concept is tied to your query in a meaningful way. In addition, the border color indicates whether the concept is trending upward (red), trending downward (blue), or has no significant change (gray).

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What is the Meaning of the Concept Connections Visualization? (For Qinsight only)
The Concept Connections visualization identifies connections between members of a Power Term® class. Instead of considering each Power Term® member one at a time, you can see how the members are related to each other, with the strength of the connection indicated by the darker color.

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My Space - FAQ

What is My Space?
The My Space pages are where your saved information, such as Saved Searches and Profile, can be accessed. You access your My Space pages by clicking the "Your Space" link at the top right of the search box (on both the Main Search page or the Results pages).

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I saved a Key Concept filter as part of a Saved Search, but I do not see that Key Concept when I re-run that search. Why not?
Key Concepts are the most relevant concepts associated with the Relevant Statements found by your search. As new documents are added to the database, an old Key Concept may become pushed down in relevance and hence no longer "key". This should be a rare occurrence, but with the rapid changes in science it is possible. If you want to limit your search results to those contained the "expired" Key Concept, simply apply that term in the Also Containing filter.

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Why don't I see a My Library link with each result?
When an article has direct PDF access, the My Library Link is not shown.

When an article does not have direct PDF access, linking to articles through your organization's journal holdings requires that your organization provides certain connecting information (including the URL for the Link Resolver). There are connections to over 1300 organizations (universities, hospitals, companies).

Go to your My Space My Profile page and select your organization from the Organization drop-down list. Then Save your Profile.

If your organization is not listed in the Organization drop-down list (that is, you have to choose Other and then enter your organization's name, then your organization has provided us with the necessary information to connect. Ask your librarian to visit the Librarian page for more information. It's quick, easy, and free.

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How do I get Alerts for my saved searches?
On your My Space Saved Searches page, simply check the checkbox for the search(es) you want Alerts for.

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Why didn't I get an Alert this Week?
An Alert is only sent if there is a newly added document that meets your saved search criteria.

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Why is there an old paper in my Alert?
You may occasionally see an older document in your My Space Alert. This can happen when that document was recently added to the databases. For example, if a new journal is added to PubMed and back issues are newly indexed, you may see an old article from that Journal if it matches your search criteria.

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Why am I asked to log in when I already did that?
If you logged in but then were inactive on the site for a while, the session "times out" to help protect your privacy. You will need to log in again.

You may also be requested to log in again if you accessed your subscription from another computer. No matter how long you were logged in on the first computer, once you log in from another computer or device any other open sessions are closed.

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Registration and Subscriptions - FAQ

How do I change to a different version?
To change which BioAI™ version you are subscribed to, log in and go to your My Space My Account page. Here you will find options to change your subscription version, the renewal period, and automatic renewals.

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How do I take advantage of my organization's subscription when I register?
If your organization has a site license, then you will see a "Happy News" message on the Welcome page. Click "register" in that message to create your account. You will not incur any fees for registering.

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Why am I asked to pay when my organization has a subscription?
You are identified as belonging to a specific organization by your IP address. So, you must be on campus or connected to your campus through a VPN connection for the organization's subscription to apply.

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Miscellaneous Issues - FAQ

Why don't some links and actions work in my browser?
Many controls - including links to the Power Term® class list require javascript to be enabled. To enjoy the full functionality of the site, you should allow javascript to run in your browser.

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© Copyright 2008-2016 Quertle, LLC. All Rights Reserved.
Quertle, "Find What Matters", "Power Term", and Quetzal are registered trademarks of Quertle LLC
Qinsight, Qdiscover, Qexplorer, Qbasic, and BioAI are trademarks of Quertle LLC